<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/3029?offset=920 https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material Sat, 18 Mar 2023 11:26:18 -0500 https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material <![CDATA[Bioinformatics Training Material !]]> Glittr is a curated list of bioinformatics training material.
All material is:

  • In a GitHub or GitLab repository
  • Free to use
  • Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

]]> BioStar https://bioinformaticsonline.com/blog/view/44516/16srna-database-download Wed, 24 Apr 2024 04:33:15 -0500 https://bioinformaticsonline.com/blog/view/44516/16srna-database-download <![CDATA[16sRNA Database Download]]> Downloading 16S rRNA databases can be crucial for various bioinformatics analyses, especially in microbiome research. However, it's important to note that databases can vary based on your specific needs, such as the taxonomic coverage you require or the type of analysis you're performing. Here's a general guideline on how you can obtain 16S rRNA databases:

  1. NCBI (National Center for Biotechnology Information):

    • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
    • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
    • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
    • You can download sequences individually or in batches using the provided tools.

  2. GreenGenes:

    • GreenGenes is a widely used 16S rRNA gene sequence database.
    • You can access it at http://greengenes.secondgenome.com/.
    • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

  3. SILVA:

    • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
    • It covers not only 16S rRNA but also other ribosomal RNA sequences.
    • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

  4. Ribosomal Database Project (RDP):

    • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
    • It provides tools for sequence analysis and classification.
    • You can download sequences and taxonomy information from their website.

  5. QIIME (Quantitative Insights Into Microbial Ecology):

    • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
    • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
    • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

 

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/852/queensland-centre-for-medical-genomics-grimmond-lab Sun, 14 Jul 2013 11:58:34 -0500 <![CDATA[Queensland Centre for Medical Genomics, Grimmond Lab]]> Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

]]> https://bioinformaticsonline.com/opportunity/view/4725/complex-systems-from-physics-to-biology-october-15-16-2013-at-jnu-convention-center Mon, 23 Sep 2013 10:17:17 -0500 <![CDATA[Complex Systems: From Physics to Biology October 15-16 2013 at JNU Convention Center]]> The symposium intents to focus on complex systems arising in a variety of settings in physics and biology. In particular, applications of the concepts of physics to biological sciences will be the major theme of this meeting.

Selected Topics:

Cluster Dynamics
Non-equilibrium Statistical Mechanics
Forced Systems
Hamiltonian Dynamics
Synchronization & Control
Genomics & Systems Biology
Computational Neuroscience
Econophysics

More @ http://www.jnu.ac.in/Conference/SCS2013/

]]> https://bioinformaticsonline.com/researchlabs/view/863/rolland-lagan-lab Sun, 14 Jul 2013 12:57:57 -0500 <![CDATA[Rolland-Lagan lab]]> The Rolland-Lagan lab at the University of Ottawa is specializing in computational and developmental biology. We use a combination of experimental work, microscopy, image analysis and computer simulations to explore developmental mechanisms in two and three dimensions.

Research Area

Developmental biology, Computational biology, Simulation modeling, Image data analysis

Link @ http://mysite.science.uottawa.ca/arolland/index.html

]]> https://bioinformaticsonline.com/file/view/18653/genetic-code-amino-acid Sun, 26 Oct 2014 07:45:58 -0500 https://bioinformaticsonline.com/file/view/18653/genetic-code-amino-acid <![CDATA[Genetic code - Amino Acid]]> The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

The image summarise all in one.

More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

]]> Poonam Mahapatra https://bioinformaticsonline.com/opportunity/view/42804/one-year-position-for-a-bioinformatician-computational-biologist-in-population-genetics Fri, 05 Feb 2021 11:19:02 -0600 <![CDATA[One-year position for a bioinformatician / computational biologist in population genetics]]> The successful candidate will work as support staff mainly in the development, application and maintenance of pipelines for handling large omics datasets (including whole-genome sequences, high-density genotypes and mRNA sequences). These pipelines cover pre-processing of data, statistical analyses and genome bioinformatics. The postholder will also provide support in producing high-level graphic representations of
these data and of results from their analysis. Our team is part of UMR
7268 ADES research unit (Anthropologie bio-culturelle, Droit, Ethique
et Sant=E9), located at the Timone Faculty of Medicine (Aix-Marseille
University, 13005 Marseille).

JOB QUALIFICATION
- PhD/Engineer/MSc in bioinformatics, biostatistics, genetics/genomics
or any related field.
- Advanced knowledge of Bash/Perl scripting and job management on a Unix
HPC and in at least one basic language for data
manipulation/statistics (such as R/Python/Matlab) are required.
- Knowledge of at least one programming language (e.g. C), experience
processing -omics data or skills in advanced graphical representation
of data would be a plus.

DURATION
1 year, not extensible

SALARY
Gross salary is commensurate with experience and grade (MSc from
1,882=80/month and PhD/equivalent from 2,099=80/month).

APPLICATIONS/OPENING
Please send a motivation letter, a CV and the names of two referees to
pierre.faux@univ-amu.fr. The expected starting date is April 1st, 2021;
the job offer will however remain opened until the position is filled.

Pierre Faux

]]> https://bioinformaticsonline.com/researchlabs/view/861/fiona-brinkman-laboratory Sun, 14 Jul 2013 12:46:31 -0500 <![CDATA[Fiona Brinkman Laboratory]]> Infectious disease control needs to be made more “sustainable”. We need to reduce selective pressure on pathogens to evolve antibiotic resistance. We need to control infectious disease outbreaks and associated immune disorders with a better understanding of the genetic, environmental and social factors that impact disease spread and severity.

Research Area

Investigating the role in disease of both the microbe and its host (i.e immune system failure), using genomics and systems biology-based approaches
Using genomics and network analysis to characterize disease outbreaks and their environmental/social/genetic causes, and
Identifying new anti-infective and immune modulating therapies/biomarkers.

Link @ http://www.brinkman.mbb.sfu.ca/

]]> https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics Tue, 16 Jul 2013 03:50:30 -0500 https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics <![CDATA[Phylogenetic for Bioinformatics]]> Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the Tree of Life. The Tree of Life then represents the phylogeny of organisms, i. e., the history of organismal lineages as they change through time.
Every living organism contains DNA, RNA, and proteins. Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures. 
phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. In other word, Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms Molecular phylogeny is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a so-called phylogenetic tree.

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

  • TNT-Tree Analysis Using New Technology
  • Tree View-Taxonomy and Systematics Group at Glasgow
]]> Jitendra Narayan https://bioinformaticsonline.com/videolist/watch/2882/phylogenetics Fri, 23 Aug 2013 03:53:43 -0500 https://bioinformaticsonline.com/videolist/watch/2882/phylogenetics <![CDATA[Phylogenetics]]> 006 - Phylogenetics Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data. A specific type of phylogenetic tree, the cladogram, is also covered. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License]]>